The following are the challenges facing Juba International Airport:
- Congestion and lack of enough space the small space available at the Airport serves as the arrivals hall, baggage collection, customs and immigration.
- Juba International Airport does not have radar capabilities and, therefore, closes at 6:00 p.m., limiting incoming and outgoing flights to daylight hours only.
- Passenger pre-flight security screening is not conducted thoroughly, and equipment is out-dated.
- Travelers who use the VIP lounge and their carry-on luggage are not screened prior to boarding flights. Diplomatic vehicles are allowed to drive onto the runway and sometimes right up to the plane for boarding and disembarking.
- South Sudan does not have a national airline, there are daily direct flights to Nairobi, Addis Ababa, Entebbe, and Cairo by multiple carriers. Most in-country air travel is conducted by UN or private chartered aircraft.
- Insufficient funds, the Civil Aviation Authority does not have sufficient funds to keep pace with the advancement in airport equipment and technology.
- Unskilled labour, there is a considerable shortage of mid-level managers and technicians in the airport sector. There is therefore an urgent need to train staff for acquire the necessary skills to enable them fill the positions.
- Low passenger numbers, South Sudan has continued to experience the problem of low passenger numbers due to political instability that was a result of civil wars before the country gained independence in 2011, however the list of airline operators is continuously growing.